"
Team:Valencia UPV/Modeling/fba
From 2014.igem.org
Alejovigno (Talk | contribs) |
|||
| Line 18: | Line 18: | ||
<div class="tab-content"> | <div class="tab-content"> | ||
<div id="tab1" class="tab active"> | <div id="tab1" class="tab active"> | ||
| - | < | + | <h2>Modeling Pheromone Production Overview</h2> |
| - | <p>Pheromones production rates are estimated when the system is in stationary state with an FBA (Flux Balance Analysis). This can be useful to know about the amount of pheromone that can be produced by the synthetic plant during a certain period of time, once the system has ended its transitory levels of pheromone production.</p> | + | <br/> |
| + | <p>Pheromones production rates are estimated when the system is in stationary state with an FBA (Flux Balance Analysis). This can be useful to know about the amount of pheromone that can be produced by the synthetic plant during a certain period of time, once the system has ended its transitory levels of pheromone production.</p><br/> | ||
<h2>Flux Balance Analysis</h2> | <h2>Flux Balance Analysis</h2> | ||
<p>Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of metabolites through a metabolic network. FBA is a widely used for studying biochemical networks, in particular the genome-scale metabolic network reconstructions that have been built in the past decade. These reconstructions contain all of the known metabolic reactions in an organism or plant, and the genes that encode each enzyme. In our case, FBA will calculate the flow of metabolites through our metabolic network to obtain the major production of pheromone.</p> | <p>Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of metabolites through a metabolic network. FBA is a widely used for studying biochemical networks, in particular the genome-scale metabolic network reconstructions that have been built in the past decade. These reconstructions contain all of the known metabolic reactions in an organism or plant, and the genes that encode each enzyme. In our case, FBA will calculate the flow of metabolites through our metabolic network to obtain the major production of pheromone.</p> | ||
| - | < | + | <h3>CROBA</h3> |
<p>The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1]. | <p>The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1]. | ||
The COBRA Toolbox [2] is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).</p> | The COBRA Toolbox [2] is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).</p> | ||
Revision as of 20:39, 12 October 2014
Modeling Pheromone Production Overview
Pheromones production rates are estimated when the system is in stationary state with an FBA (Flux Balance Analysis). This can be useful to know about the amount of pheromone that can be produced by the synthetic plant during a certain period of time, once the system has ended its transitory levels of pheromone production.
Flux Balance Analysis
Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of metabolites through a metabolic network. FBA is a widely used for studying biochemical networks, in particular the genome-scale metabolic network reconstructions that have been built in the past decade. These reconstructions contain all of the known metabolic reactions in an organism or plant, and the genes that encode each enzyme. In our case, FBA will calculate the flow of metabolites through our metabolic network to obtain the major production of pheromone.
CROBA
The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism or plant at the genome scale [1]. The COBRA Toolbox [2] is a freely available Matlab toolbox can be used to perform a variety of COBRA methods, including many FBA-based methods. Models for the COBRA Toolbox are saved in the Systems Biology Markup Language (SBML).
NetLogo is an agent-based programming language and integrated modeling environment. NetLogo is free and open source software, under a GPL license.
NetLogo is an agent-based programming language and integrated modeling environment. NetLogo is free and open source software, under a GPL license.
Tab #4 content goes here!
Donec pulvinar neque sed semper lacinia. Curabitur lacinia ullamcorper nibh; quis imperdiet velit eleifend ac. Donec blandit mauris eget aliquet lacinia! Donec pulvinar massa interdum risus ornare mollis. In hac habitasse platea dictumst. Ut euismod tempus hendrerit. Morbi ut adipiscing nisi. Etiam rutrum sodales gravida! Aliquam tellus orci, iaculis vel.
